12-95461400-C-T

Position:

• chr12-95461400-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.111 in 150,426 control chromosomes in the GnomAD database, including 959 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (959 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16624 AN: 150318 Hom.: 961 Cov.: 29

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.0431

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.0819

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0854

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.111 AC: 16637 AN: 150426 Hom.: 959 Cov.: 29 AF XY: 0.110 AC XY: 8047 AN XY: 73430

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0652

Gnomad4 ASJ AF: 0.0431

Gnomad4 EAS AF: 0.0419

Gnomad4 SAS AF: 0.0820

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0845

Alfa AF: 0.113 Hom.: 504

Bravo AF: 0.107

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs964496; hg19: chr12-95855176;